Time Series Input Selection using Multiple Kernel Learning

In this paper we study the relevance of multiple kernel learning (MKL) for the automatic selection of time series inputs. Recently, MKL has gained great attention in the machine learning community due to its flexibility in modelling complex patterns and performing feature selection. In general, MKL constructs the kernel as a weighted linear combination of basis kernels, exploiting different sources of information. An efficient algorithm wrapping a Support Vector Regression model for optimizing the MKL weights, named SimpleMKL, is used for the analysis. In this sense, MKL performs feature selection by discarding inputs/kernels with low or null weights. The approach proposed is tested with simulated linear and nonlinear time series (AutoRegressive, Henon and Lorenz series).

Myocardial flow reserve by Rb-82 cardiac PET improves the selection of patients eligible for invasive coronary angiography

Aim: We asked whether myocardial flow reserve (MFR) by Rb-82 cardiac PET improve the selection of patients eligible for invasive coronary angiography (ICA). Material and Methods: We enrolled 26 consecutive patients with suspected or known coronary artery disease who performed dynamic Rb-82 PET/CT and (ICA) within 60 days; 4 patients who underwent revascularization or had any cardiovascular events between PET and ICA were excluded. Myocardial blood flow at rest (rMBF), at stress with adenosine (sMBF) and myocardial flow reserve (MFR=sMBF/rMBF) were estimated using the 1-compartment Lortie model (FlowQuant) for each coronary arteries territories. Stenosis severity was assessed using computer-based automated edge detection (QCA). MFR was divided in 3 groups: G1:MFR<1.5, G2:1.5≤MFR<2 and G3:2≤MFR. Stenosis severity was graded as non-significant (<50% or FFR ≥0.8), intermediate (50%≤stenosis<70%) and severe (≥70%). Correlation between MFR and percentage of stenosis were assessed using a non-parametric Spearman test. Results: In G1 (44 vessels), 17 vessels (39%) had a severe stenosis, 11 (25%) an intermediate one, and 16 (36%) no significant stenosis. In G2 (13 vessels), 2 (15%) vessels presented a severe stenosis, 7 (54%) an intermediate one, and 4 (31%) no significant stenosis. In G3 (9 vessels), 0 vessel presented a severe stenosis, 1 (11%) an intermediate one, and 8 (89%) no significant stenosis. Of note, among 11 patients with 3-vessel low MFR<1.5 (G1), 9/11 (82%) had at least one severe stenosis and 2/11 (18%) had at least one intermediate stenosis. There was a significant inverse correlation between stenosis severity and MFR among all 66 territories analyzed (rho= -0.38, p=0.002). Conclusion: Patients with MFR>2 could avoid ICA. Low MFR (G1, G2) on a vessel-based analysis seems to be a poor predictor of severe stenosis severity. Patients with 3-vessel low MFR would benefit from ICA as they are likely to present a significant stenosis in at least one vessel.

The role of gene duplication in the origin and evolution of new biological functions

Abstract : Gene duplication is an essential source of material for the origin of genetic novelty and the evolution of lineage- or species-specific phenotypic traits. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with a significant number of gene copies during the last ~63 million years (MYA) of primate evolution. We estimated that at least 1 new functional gene (retrogene) per MYA emerged by retroposition in the primate lineage leading to humans. Using a combination of comparative sequencing and evolutionary simulations, we obtained strong evidence of functionality for 7 primate specific retrogenes. Most of these genes are specifically expressed in testis suggesting that retroposition has contributed with genetic raw material necessary for the evolution ofmale-specific functions in primates. We characterized CDC14Bretro (identified in the previous survey) that originated from the retroposition of a cell cycle gene - CDC14B - in the common ancestor of humans and apes. We demonstrate that CDC14Bretro experienced a period of intense positive selection in the African ape ancestor. By virtue of the amino acid substitutions that occurred during this period CDC 14Bretro adapted to a new subcellular compartment in African apes. Further analyses indicate that this subcellular shift reflects the evolution of anew functional role of CDC 14Bretro. Prompted by this result, we used yeast (Saccharomyces cerevisiae) to investigate on a global scale the extent of functional diversification of duplicate genes through the subcellular adaptation of their encoded proteins. We found that duplicate proteins frequently evolved new cellular localization patterns, either by partitioning of ancestral localizations ("sublocalization"), or more frequently by relocalization to previously unoccupied compartments ("neolocalization"). Interestingly, proteins involved in processes with a wider subcellular distribution more frequently evolved new localization patterns suggesting that subcellular localization changes are dependent on progenitor gene functions. Relocated proteins adapted to their new subcellular environments and evolved new functional roles through changes of their physio-chemical properties, expression levels, and interaction partners. Our work suggests an important role of subcellular adaptation for the emergence of new gene functions.

Genetic team composition and level of selection in the evolution of cooperation

In cooperative multiagent systems, agents interac to solve tasks. Global dynamics of multiagent teams result from local agent interactions, and are complex and difficult to predict. Evolutionary computation has proven a promising approach to the design of such teams. The majority of current studies use teams composed of agents with identical control rules ("geneti- cally homogeneous teams") and select behavior at the team level ("team-level selection"). Here we extend current approaches to include four combinations of genetic team composition and level of selection. We compare the performance of genetically homo- geneous teams evolved with individual-level selection, genetically homogeneous teams evolved with team-level selection, genetically heterogeneous teams evolved with individual-level selection, and genetically heterogeneous teams evolved with team-level selection. We use a simulated foraging task to show that the optimal combination depends on the amount of cooperation required by the task. Accordingly, we distinguish between three types of cooperative tasks and suggest guidelines for the optimal choice of genetic team composition and level of selection

Lineage potential, plasticity and environmental reprogramming of epithelial stem/progenitor cells.

Recent evidence supports and reinforces the concept that environmental cues may reprogramme somatic cells and change their natural fate. In the present review, we concentrate on environmental reprogramming and fate potency of different epithelial cells. These include stratified epithelia, such as the epidermis, hair follicle, cornea and oesophagus, as well as the thymic epithelium, which stands alone among simple and stratified epithelia, and has been shown recently to contain stem cells. In addition, we briefly discuss the pancreas as an example of plasticity of intrinsic progenitors and even differentiated cells. Of relevance, examples of plasticity and fate change characterize pathologies such as oesophageal metaplasia, whose possible cell origin is still debated, but has important implications as a pre-neoplastic event. Although much work remains to be done in order to unravel the full potential and plasticity of epithelial cells, exploitation of this phenomenon has already entered the clinical arena, and might provide new avenues for future cell therapy of these tissues.

Large-scale evolutionary trends of Acrochordiceratidae Arthaber, 1911 (Ammonoidea, Middle Triassic) and Cope's rule

Directed evolution of life through millions of years, such as increasing adult body size, is one of the most intriguing patterns displayed by fossil lineages. Processes and causes of such evolutionary trends are still poorly understood. Ammonoids (externally shelled marine cephalopods) are well known to have experienced repetitive morphological evolutionary trends of their adult size, shell geometry and ornamentation. This study analyses the evolutionary trends of the family Acrochordiceratidae Arthaber, 1911 from the Early to Middle Triassic (251228 Ma). Exceptionally large and bed-rock-controlled collections of this ammonoid family were obtained from strata of Anisian age (Middle Triassic) in north-west Nevada and north-east British Columbia. They enable quantitative and statistical analyses of its morphological evolutionary trends. This study demonstrates that the monophyletic clade Acrochordiceratidae underwent the classical evolute to involute evolutionary trend (i.e. increasing coiling of the shell), an increase in its shell adult size (conch diameter) and an increase in the indentation of its shell suture shape. These evolutionary trends are statistically robust and seem more or less gradual. Furthermore, they are nonrandom with the sustained shift in the mean, the minimum and the maximum of studied shell characters. These results can be classically interpreted as being constrained by the persistence and common selection pressure on this mostly anagenetic lineage characterized by relatively moderate evolutionary rates. Increasing involution of ammonites is traditionally interpreted by increasing adaptation mostly in terms of improved hydrodynamics. However, this trend in ammonoid geometry can also be explained as a case of Copes rule (increasing adult body size) instead of functional explanation of coiling, because both shell diameter and shell involution are two possible paths for ammonoids to accommodate size increase.

The role of Notch signaling during hematopoietic lineage commitment.

Over the last few years a vast amount of progress has been made in identifying mechanisms controlling lineage commitment and plasticity of hematopoietic precursors to different lymphoid or myeloid lineages. This has been due largely to the ability to identify and isolate rare cell populations in order to investigate their developmental potential, together with the development of inducible and/or tissue specific targeting technology. One family of proteins that has been postulated to be involved in hematopoietic stem cell maintenance as well as in multiple commitment processes during T cell development is the Notch receptors and their ligands. In this review we will summarize recent findings and controversies regarding the role of Notch signaling in the myeloid and lymphoid systems.

Sex allocation and sex-dependent selection for body size in Trypoxylon rogenhoferi Kohl (Hymenoptera, Sphecidae)

Two populations of the wasp Trypoxylon rogenhoferi Kohl, 1884 from São Carlos and Luís Antônio, State of São Paulo, Brazil, were observed and sampled from May 1999 to February 2001 using trap-nests. This mass-provisioning wasp was used to test some aspects of optimal sex allocation theory. Both populations fit all the predictions of the models of Green and Brockmann and Grafen. Maternal provisions determined the size of each offspring, and females allocated well-stocked brood cells to daughters, the sex that benefits most being large. This strategy resulted in a difference in size between the sexes. In São Carlos, female weight at emergence was 1.18 times that of males, in Luís Antônio this value was 1.13. The brood cell volume was correlated with both wing length and weight at emergence in both sexes, and the chance that a given brood cell contained a male offspring decreased with increased brood cell volume. In T. rogenhoferi female body size was related to fitness. Larger females were able to collect more mass of spiders per day, the spiders they captured were heavier, and they provisioned more brood cells per day. They also produced larger daughters. For males, no relationship between body size and fitness was found, but the data were scarce. Since the patterns of provisioning were variable among different females in both study sites, it is possible that the females not follow a unique strategy for sex allocation. The sex ratio and/or investment ratio in the São Carlos population was female-biased and in Luís Antônio, male-biased. In spite of the influence of trap-nests diameters on male production in Luís Antônio, there is some evidence that in São Carlos population the local availability of prey and/or lower rate of parasitism may be major forces in determining the observed sex ratio, but further studies are necessary to verify such hypothesis.

Interviews and adverse selection

Interviewing in professional labor markets is a costly process for firms. Moreover, poor screening can have a persistent negative impact on firms bottom lines and candidates careers. In a simple dynamic model where firms can pay a cost to interview applicants who have private information about their own ability, potentially large inefficiencies arise from information-based unemployment, where able workers are rejected by firms because of their lack of offers in previous interviews. This effect may make the market less efficient than random matching. We show that the first best can be achieved using either a mechanism with transfers or one without transfers.

Influence of male nutritional conditions on the performance and alimentary selection of wild females of Anastrepha obliqua (Macquart)(Diptera, Tephritidae)

Influence of male nutritional conditions on the performance and alimentary selection of wild females of Anastrepha obliqua (Macquart) (Diptera, Tephritidae). The behavior of A. obliqua females is regulated by endogenous and exogenous factors and among these the presence of males. Experiments were carried out to investigate whether the presence of males and their nutritional condition may affect the behavior of self-selection feeding and the performance of A. obliqua females. Females were sorted in groups containing yeast-deprived females and males, and non-yeast-deprived females and males. The females were maintained apart from the males by a transparent plastic screen. Several yeast and sucrose combinations were offered to the females in a single diet block or in separate blocks. Ingestion, egg production, longevity and diet efficiency were determined. The non-yeast-deprived males positively influenced the females performance when the latter were fed with yeast and sucrose in distinct diet blocks. Performance was better in the groups without males and with yeast-deprived males where the females could not select the nutrient proportions (yeast and sucrose in a single diet block).